- modeller_usage - salilab.org

_modeller.ModellerError: getpdf__389E> MDT table range is too small. MDT should be derived with the full range of possible values for the independent variables.
by Rana Rehan Khalid 06 May '24

06 May '24

Dear Modeller Users, I am currently attempting to generate various mutant models using the MutantBuilder script available at https://github.com/eved1018/MutantBuilder. I have installed Modeller10.5 for this purpose. However, I am encountering the following issue: python3 MutantBuilder.py -pdb complex.pdb -c B Traceback (most recent call last): File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 372, in <module> main() File "/home/rehan/Downloads/… [View More]

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my automodel run well serial, but molpdf is inmediatly exceeded when run in parallel
by Mario Bianchet 16 Apr '24

16 Apr '24

Hello All The script below exceeds molpdf limits immediately when run this automodel job on parallel, but run starts with a low molpdf and ends well when commenting the line "a.use_parallel_job(j)" Any hint of how to solve will be appreciate? Mario from modelito import MyModel from modeller.parallel import * icycle=50 log.minimal() # request minimal output env = Environ() # create a new MODELLER environment to build this model in icycle=str(int(icycle)+1) # directories for input atom … [View More]

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Re: About the error ( UnicodeDecodeError: 'utf-8' codec can't decode)form logger.py
by Modeller Caretaker 16 Apr '24

16 Apr '24

On 4/16/24 8:22 AM, c00jsw00 wrote: > thanks for your help. When I use win 11 (anaconda powershell) to run a > simple python input and got the error. ... > File "D:\conda\Library\modeller\modlib\modeller\util\logger.py", line 8, > in Logger > _header = _modeller.mod_header_get() > ^^^^^^^^^^^^^^^^^^^^^^^^^^ > UnicodeDecodeError: 'utf-8' codec can't decode byte 0xaa in position > 957: invalid start byte Ah, I see the problem. It is trying to print the start of … [View More]

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About the error ( UnicodeDecodeError: 'utf-8' codec can't decode)form logger.py
by c00jsw00＠kmu.edu.tw 15 Apr '24

15 Apr '24

Dear all, When I use conda to install modller 10.4 or 10.5, I used the python (3.9) to run a simple command (from modeller import *). Then I got the error (UnicodeDecodeError: 'utf-8' codec can't decode...) . Could you tell me how to overcome it ? THX YT

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Perodic boundary condition?
by Qizan Chen 05 Apr '24

05 Apr '24

Can the Modeller take periodic boundary conditions into account during modeling? I aim to construct a condensed model, but currently, unwarping the protein to the Modeller and then warping it back leads to incorrect overlaps of side chains. I noticed that symmetry constraints can be added, but my original system is already large, and adding additional images causes crashes.

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Error identifying new atomtypes in $RADII_LIB while adding new residue into modeller topology library
by Neeraj Kumar T . 21 Mar '24

21 Mar '24

I've been trying to add a new residue's (ligand) topology and parameters into modeller library to model accurately. I am following the steps in modeller's FAQ #8: https://salilab.org/modeller/FAQ.html#8. After adding the topology into a copy of "top_heav.lib", and parameters into a copy of "par.lib", and also into copies of "radii.lib" and "solv.lib", I still get errors. This is the initial script I used: ------------------ [image: image.png] -------------------- The above script gives error … [View More]

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Modelling based on two templates - one oligomer and one monomer
by hmad3＠cam.ac.uk 19 Mar '24

19 Mar '24

Hello, I am trying to model a multichain protein using 2 templates - the .pdb file of an oligomer (with the same number of chains as the target) and the .pdb file of the AlphaFold structure of one of the monomers making up the target protein. (When I model using only the oligomer as target, the model of the target looks quite "off".) First scenario: * target protein: 5 of the same chain * template protein 1 ("base template"): a homopentamer * template protein 2 ("sub-template" - i.e. the … [View More]

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Alignment to use when I am modelling a heteromer using a homer as template
by hmad3＠cam.ac.uk 18 Mar '24

18 Mar '24

Hello, I am currently modelling a heteromeric protein using a homomeric protein as a template, as follows: - heteromer subunits (target): 2 x aaaaaaaa + bbbbbbbbb - homomer subunits (template): 3 x cccccccccc When aligning the monomer sequences to be used in the .ali file, should I align aaaaaaaa and cccccccccc separately, then bbbbbbbbb and cccccccccc and use the sequences generated in the FASTA file of each alignment in the .ali file -- or should I align all three sequences at once and use … [View More]

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I don't want to use one region of a *target* for construction of my model.
by hmad3＠cam.ac.uk 12 Mar '24

12 Mar '24

Hello, I am modelling a pentameric protein based on a template with missing residues, e.g. aaaaabbbbbdddddeeeee (except the original protein sequence has "ccccc" corresponding to a long disordered region between the "b" and "d", but this is not modelled, hence the FASTA of the protein looks like the above, and the .pdb file and 3D model of the protein would show "missing residues" between "b" and "d") The original sequence of the target protein is: fffffggggghhhhhiiiiijjjjj except "iiiii" is … [View More]

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Modeller 10.5 release
by Modeller Caretaker 23 Jan '24

23 Jan '24

A new version of Modeller, 10.5, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 9 or 10, there is no need to reregister for Modeller 10.5 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.5 is a minor update that adds support for Python 3.12, improves the mmCIF output, and adds initial support for new-style 12-character PDB IDs. If you … [View More]

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